A lot of people need to be careful when combining two words without any thought to flow. If a word feels like it needs two emphasized syllables, that's bad. Stuff like Cuprapilar (KOO-pra-PILL-ar? it actually reads like PIE-lar because of the dropped l in pillar), Agugoon (AH-goo-GOON), Cutiepilar (KEW-tee-PIE-lar again reads like pie because of the dropped l) all really doesn't work for me.
For the first stage I think the Cupru- and Cupra- roots are very unnatural (though they are kind of nice alone!). For the second stage I think the -oon/goon/coon endings really don't work at all. They are too round/soft sounding for the pokemon and coon is too distractingly like raccoon.
I like Cupa and Grubrum for the first stage, they are cute and simple and don't feel forced. I don't think worrying about the first stage not being a pupa is a problem, you could argue the 'a' is from larva.